Epitaxial growth is a very important step in a design process of a semiconductor device. For example, it is one of the key factors for a device to achieve a complex charge balance. However, during an actual manufacturing process, the epitaxial growth may distort or shift the surface geometries of various parts in the semiconductor device defined by a lithography process and an etching process. The distortion of the semiconductor device will impact the subsequent processes in terms of alignment and overlay control uncertainty. The existing technologies cannot accurately detect shape deformation factors induced by the epitaxial growth. Especially, the existing technologies cannot accurately point out impact mechanisms of the epitaxial growth environment and the corresponding process parameters associated with shape deformation factors. It leads to the failure of effectively implementing an epitaxial process optimization. Epitaxial growth induced feature magnification can be quantified by available Critical Dimension metrology, such as optical detection or SEM. The quantification may be achieved by comparing the feature sizes before the pre-epitaxial growth with the feature sizes after the post-epitaxial growth. However, there is no existing solution for monitoring the epitaxial growth geometry shift. For example, there is no known method to determine whether an original alignment mark made on a substrate's surface before the epitaxial growth and the retained alignment mark on the epitaxial layer formed after the epitaxial growth are completely overlapped, or whether there is any shift between the retained alignment mark on the epitaxial layer and the original alignment marks on the substrate.